Biospeciman Analysis Core

ABSTRACT: Biospecimen Analysis Core The Biospecimen Analysis Core will drive the development of virome data from samples acquired by the Biospecimen Collection Core of the Penn VCC. The Biospecimen Analysis Core will be led by Dr. Frederic Bushman at Penn and Dr. Ahmed Moustafa at CHOP, together with co-I Dr. Gary Wu. All have published multiple papers together, and work together closely in managing the PennCHOP Microbiome Program. The Biospecimen Analysis Core will work closely with the Penn VCC Biospecimen Collection Core to analyze samples collected from multiple body sites of children and adults, emphasizing joint analysis of oral, respiratory, gut and blood specimens. The approach will combine biobanked samples from existing cohorts with prospective resampling from many of the same individuals, allowing very long term longitudinal assessment. The Penn VCC has samples in hand for analysis over the first two years of the program, enabling immediate startup and data generation, and will turn to newly collected samples in years 3-5. The Biospecimen Analysis Core will carry out sequence analysis of purified virome specimens, and also metagenomic analysis of specimens by both whole genome shotgun sequencing and in selected low biomass samples also 16S rRNA gene sequencing. The Biospecimen Analysis Core will also carry out long read single molecule sequencing, including analyzing phage covalent DNA modification, and HiC to assign phages to hosts. The Core will also lead exploratory imaging studies. Thus we will address a wealth of questions on the nature and function of the human virome, while advancing the goals of the full HVP. The overall approach of the Biospecimen Analysis Core will be to: Aim 1. Optimize methods and validate procedures for sequence-based analysis of the virome and the background host microbiome. Aim 2. Generate sequence data on the virome and the full microbiome. Aim 3. Explore potential insights from additional methods including long read single molecule sequencing, HiC, imaging and others.